Chemical sensor with sidewall spacer sensor surface

ABSTRACT

In one implementation, a chemical sensor is described. The chemical sensor includes chemically-sensitive field effect transistor including a floating gate conductor having an upper surface. A dielectric material defines an opening extending to the upper surface of the floating gate conductor. A conductive sidewall spacer is on a sidewall of the opening and contacts the upper surface of the floating gate conductor.

BACKGROUND

The present disclosure relates to sensors for chemical analysis, and tomethods for manufacturing such sensors.

A variety of types of chemical sensors have been used in the detectionof chemical processes. One type is a chemically-sensitive field effecttransistor (chemFET). A chemFET includes a source and a drain separatedby a channel region, and a chemically sensitive area coupled to thechannel region. The operation of the chemFET is based on the modulationof channel conductance, caused by changes in charge at the sensitivearea due to a chemical reaction occurring nearby. The modulation of thechannel conductance changes the threshold voltage of the chemFET, whichcan be measured to detect and/or determine characteristics of thechemical reaction. The threshold voltage may for example be measured byapplying appropriate bias voltages to the source and drain, andmeasuring a resulting current flowing through the chemFET. As anotherexample, the threshold voltage may be measured by driving a knowncurrent through the chemFET, and measuring a resulting voltage at thesource or drain.

An ion-sensitive field effect transistor (ISFET) is a type of chemFETthat includes an ion-sensitive layer at the sensitive area. The presenceof ions in an analyte solution alters the surface potential at theinterface between the ion-sensitive layer and the analyte solution, dueto the protonation or deprotonation of surface charge groups caused bythe ions present in the analyte solution. The change in surfacepotential at the sensitive area of the ISFET affects the thresholdvoltage of the device, which can be measured to indicate the presenceand/or concentration of ions within the solution.

Arrays of ISFETs may be used for monitoring chemical reactions, such asDNA sequencing reactions, based on the detection of ions present,generated, or used during the reactions. See, for example, U.S. Pat. No.7,948,015 to Rothberg et al., which is incorporated by reference herein.More generally, large arrays of chemFETs or other types of chemicalsensors may be employed to detect and measure static and/or dynamicamounts or concentrations of a variety of analytes (e.g. hydrogen ions,other ions, compounds, etc.) in a variety of processes. The processesmay for example be biological or chemical reactions, cell or tissuecultures or monitoring neural activity, nucleic acid sequencing, etc.

An issue that arises in the operation of large scale chemical sensorarrays is the susceptibility of the sensor output signals to noise.Specifically, the noise affects the accuracy of the downstream signalprocessing used to determine the characteristics of the chemical and/orbiological process being detected by the sensors.

It is therefore desirable to provide devices including low noisechemical sensors, and methods for manufacturing such devices.

SUMMARY

In one implementation, a chemical sensor is described. The chemicalsensor includes a chemically-sensitive field effect transistor includinga floating gate conductor having an upper surface. A dielectric materialdefines an opening extending to the upper surface of the floating gateconductor. A conductive sidewall spacer is on a sidewall of the openingand contacts the upper surface of the floating gate conductor.

In another implementation, a method for manufacturing a chemical sensoris described. The method includes forming a chemically-sensitive fieldeffect transistor including a floating gate conductor having an uppersurface. The method further includes forming a dielectric materialdefining an opening extending to the upper surface of the floating gateconductor. The method further includes forming a conductive sidewallspacer on a sidewall of the opening and contacting the floating gateconductor.

Particular aspects of one more implementations of the subject matterdescribed in this specification are set forth in the drawings and thedescription below. Other features, aspects, and advantages of thesubject matter will become apparent from the description, the drawings,and the claims.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 illustrates a block diagram of components of a system for nucleicacid sequencing according to an exemplary embodiment.

FIG. 2 illustrates a cross-sectional view of a portion of the integratedcircuit device and flow cell according to an exemplary embodiment.

FIGS. 3A and 3B illustrate cross-sectional and plan views respectivelyof a representative chemical sensors and corresponding reaction regionsaccording to an exemplary embodiment.

FIGS. 4 to 7 illustrate stages in a manufacturing process for forming anarray of chemical sensors and corresponding well structures according toan exemplary embodiment.

DETAILED DESCRIPTION

A chemical detection device is described that includes low noisechemical sensors, such as chemically-sensitive field effect transistors(chemFETs), for detecting chemical reactions within overlying,operationally associated reaction regions.

Reducing the plan or top view area (or footprint) of individual chemicalsensors and the overlying reaction regions allows for higher densitydevices. However, as the dimensions of the chemical sensors are reduced,Applicants have found that a corresponding reduction in the sensingsurface area of the sensors can significantly impact performance.

For example, for chemical sensors having sensing surfaces defined at thebottom of the reaction regions, reducing the plan view dimensions (e.g.the width or diameter) of the reaction regions results in a similarreduction in the sensing surface areas. Applicants have found that asthe sensing surface area is reduced to technology limits, fluidic noisedue to the random fluctuation of charge on the sensing surfacecontributes to an increasing proportion of the total variation insensing surface potential. This can significantly reduce thesignal-to-noise ratio (SNR) of the sensor output signal, which affectsthe accuracy of the downstream signal processing used to determine thecharacteristics of the chemical and/or biological process being detectedby the sensor.

Chemical sensors described herein have sensing surface areas which arenot limited to a two-dimensional area at the bottom of the reactionregions. In embodiments described herein, the sensing surface of thechemical sensor includes a generally horizontal portion along the bottomsurface of the reaction region, as well as a generally vertical portionprovided by a sidewall spacer on a sidewall of the reaction region.

By extending the sensing surface in a generally vertical direction, thechemical sensor can have a small footprint, while also having asufficiently large sensing surface area to avoid the noise issuesassociated with small sensing surfaces. The footprint of a chemicalsensor is determined in part by the width (e.g. diameter) of theoverlying reaction region and can be made small, allowing for a highdensity array. In addition, because the sensing surface extends up thesidewall, the sensing surface area can be relatively large. As a result,low noise chemical sensors can be provided in a high density array, suchthat the characteristics of reactions can be accurately detected.

FIG. 1 illustrates a block diagram of components of a system for nucleicacid sequencing according to an exemplary embodiment. The componentsinclude a flow cell 101 on an integrated circuit device 100, a referenceelectrode 108, a plurality of reagents 114 for sequencing, a valve block116, a wash solution 110, a valve 112, a fluidics controller 118, lines120/122/126, passages 104/109/111, a waste container 106, an arraycontroller 124, and a user interface 128. The integrated circuit device100 includes a microwell array 107 overlying a sensor array thatincludes chemical sensors as described herein. The flow cell 101includes an inlet 102, an outlet 103, and a flow chamber 105 defining aflow path of reagents over the microwell array 107.

The reference electrode 108 may be of any suitable type or shape,including a concentric cylinder with a fluid passage or a wire insertedinto a lumen of passage 111. The reagents 114 may be driven through thefluid pathways, valves, and flow cell 101 by pumps, gas pressure, orother suitable methods, and may be discarded into the waste container106 after exiting the outlet 103 of the flow cell 101. The fluidicscontroller 118 may control driving forces for the reagents 114 and theoperation of valve 112 and valve block 116 with suitable software.

The microwell array 107 includes an array of reaction regions asdescribed herein, also referred to herein as microwells, which areoperationally associated with corresponding chemical sensors in thesensor array. For example, each reaction region may be coupled to achemical sensor suitable for detecting an analyte or reaction propertyof interest within that reaction region. The microwell array 107 may beintegrated in the integrated circuit device 100, so that the microwellarray 107 and the sensor array are part of a single device or chip.

The flow cell 101 may have a variety of configurations for controllingthe path and flow rate of reagents 114 over the microwell array 107. Thearray controller 124 provides bias voltages and timing and controlsignals to the integrated circuit device 100 for reading the chemicalsensors of the sensor array. The array controller 124 also provides areference bias voltage to the reference electrode 108 to bias thereagents 114 flowing over the microwell array 107.

During an experiment, the array controller 124 collects and processesoutput signals from the chemical sensors of the sensor array throughoutput ports on the integrated circuit device 100 via bus 127. The arraycontroller 124 may be a computer or other computing means. The arraycontroller 124 may include memory for storage of data and softwareapplications, a processor for accessing data and executing applications,and components that facilitate communication with the various componentsof the system in FIG. 1.

The values of the output signals of the chemical sensors indicatephysical and/or chemical parameters of one or more reactions takingplace in the corresponding reaction regions in the microwell array 107.For example, in an exemplary embodiment, the values of the outputsignals may be processed using the techniques disclosed in Rearick etal., U.S. patent application Ser. No. 13/339,846, filed Dec. 29, 2011,based on U.S. Prov. Pat. Appl. Nos. 61/428,743, filed Dec. 30, 2010, and61/429,328, filed Jan. 3, 2011, and in Hubbell, U.S. patent applicationSer. No. 13/339,753, filed Dec. 29, 2011, based on U.S. Prov. Pat. Appl.No. 61/428,097, filed Dec. 29, 2010, which are all incorporated byreference herein in their entirety.

The user interface 128 may display information about the flow cell 101and the output signals received from chemical sensors in the sensorarray on the integrated circuit device 100. The user interface 128 mayalso display instrument settings and controls, and allow a user to enteror set instrument settings and controls.

In an exemplary embodiment, during the experiment the fluidicscontroller 118 may control delivery of the individual reagents 114 tothe flow cell 101 and integrated circuit device 100 in a predeterminedsequence, for predetermined durations, at predetermined flow rates. Thearray controller 124 can then collect and analyze the output signals ofthe chemical sensors indicating chemical reactions occurring in responseto the delivery of the reagents 114.

During the experiment, the system may also monitor and control thetemperature of the integrated circuit device 100, so that reactions takeplace and measurements are made at a known predetermined temperature.

The system may be configured to let a single fluid or reagent contactthe reference electrode 108 throughout an entire multi-step reactionduring operation. The valve 112 may be shut to prevent any wash solution110 from flowing into passage 109 as the reagents 114 are flowing.Although the flow of wash solution may be stopped, there may still beuninterrupted fluid and electrical communication between the referenceelectrode 108, passage 109, and the microwell array 107. The distancebetween the reference electrode 108 and the junction between passages109 and 111 may be selected so that little or no amount of the reagentsflowing in passage 109 and possibly diffusing into passage 111 reach thereference electrode 108. In an exemplary embodiment, the wash solution110 may be selected as being in continuous contact with the referenceelectrode 108, which may be especially useful for multi-step reactionsusing frequent wash steps.

FIG. 2 illustrates cross-sectional and expanded views of a portion ofthe integrated circuit device 100 and flow cell 101. During operation,the flow chamber 105 of the flow cell 101 confines a reagent flow 208 ofdelivered reagents across open ends of the reaction regions in themicrowell array 107. The volume, shape, aspect ratio (such as basewidth-to-well depth ratio), and other dimensional characteristics of thereaction regions may be selected based on the nature of the reactiontaking place, as well as the reagents, byproducts, or labelingtechniques (if any) that are employed.

The chemical sensors of the sensor array 205 are responsive to (andgenerate output signals) chemical reactions within associated reactionregions in the microwell array 107 to detect an analyte or reactionproperty of interest. The chemical sensors of the sensor array 205 mayfor example be chemically sensitive field-effect transistors (chemFETs),such as ion-sensitive field effect transistors (ISFETs). Examples ofchemical sensors and array configurations that may be used inembodiments are described in U.S. Patent Application Publication No.2010/0300559, No. 2010/0197507, No. 2010/0301398, No. 2010/0300895, No.2010/0137143, and No. 2009/0026082, and U.S. Pat. No. 7,575,865, eachwhich are incorporated by reference herein.

FIG. 3A illustrates a cross-sectional view of two representativechemical sensors and their corresponding reaction regions according toan exemplary embodiment. In FIG. 3, two chemical sensors 350, 351 areshown, representing a small portion of a sensor array that can includemillions of chemical sensors.

Chemical sensor 350 is coupled to corresponding reaction region 301, andchemical sensor 351 is coupled to corresponding reaction region 302.Chemical sensor 350 is representative of the chemical sensors in thesensor array. In the illustrated example, the chemical sensor 350 is achemically-sensitive field effect transistor (chemFET), morespecifically an ion-sensitive field effect transistor (ISFET) in thisexample.

The chemical sensor 350 includes a floating gate structure 318 having asensor plate 320 underlying the reaction region 301. As can be seen inFIG. 3A, the sensor plate 320 is the uppermost floating gate conductorin the floating gate structure 318. In the illustrated example, thefloating gate structure 318 includes multiple patterned layers ofconductive material within layers of dielectric material 319.

The chemical sensor 350 also includes a source region 321 and a drainregion 322 within a semiconductor substrate 354. The source region 321and the drain region 322 comprise doped semiconductor material have aconductivity type different from the conductivity type of the substrate354. For example, the source region 321 and the drain region 322 maycomprise doped P-type semiconductor material, and the substrate maycomprise doped N-type semiconductor material.

Channel region 323 separates the source region 321 and the drain region322. The floating gate structure 318 overlies the channel region 323,and is separated from the substrate 354 by a gate dielectric 352. Thegate dielectric 352 may be for example silicon dioxide. Alternatively,other dielectrics may be used for the gate dielectric 352.

As shown in FIG. 3A, the reaction region 301 is within an opening havinga sidewall 303 extending through dielectric material 310 to the uppersurface 331 of the sensor plate 320. The dielectric material 310 maycomprise one or more layers of material, such as silicon dioxide orsilicon nitride.

The dimensions of the openings, and their pitch, can vary fromimplementation to implementation. In some embodiments, the openings canhave a characteristic diameter, defined as the square root of 4 timesthe plan view cross-sectional area (A) divided by Pi (e.g., sqrt(4*A/π),of not greater than 5 micrometers, such as not greater than 3.5micrometers, not greater than 2.0 micrometers, not greater than 1.6micrometers, not greater than 1.0 micrometers, not greater than 0.8micrometers, not greater than 0.6 micrometers, not greater than 0.4micrometers, not greater than 0.2 micrometers or even not greater than0.1 micrometers.

The chemical sensor 350 includes an electrically conductive sidewallspacer 370 on the sidewall 303 of the dielectric material 310. In theillustrated embodiment, the inner surface 371 of the conductive sidewallspacer 370 is an outer surface of the reaction region 301. In addition,the upper surface 331 of the sensor plate 320 is a bottom surface of thereaction region 301. That is, there is no intervening deposited materiallayer between the inner surface 371 of the conductive sidewall spacer370 and the reaction region 301, or between the upper surface 331 of thesensor plate 320 and the reaction region 301. As a result of thisstructure, the upper surface 331 of the sensor plate 320 and the innersurface 371 of the conductive sidewall spacer 370 is cup-shaped and actsas the sensing surface of the chemical sensor 350. The sensor plate 320and the sidewall spacer 370 may each comprise one or more of a varietyof different materials to facilitate sensitivity to particular ions(e.g. hydrogen ions).

The cup-shaped sensing surface allows the chemical sensor 350 to have asmall plan view area, while also having a sufficiently large surfacearea to avoid the noise issues associated with small sensing surfaces.The plan view area of the chemical sensor is determined in part by thewidth (or diameter) of the reaction region 301 and can be made small,allowing for a high density array. In addition, because the sensingsurface extends up the sidewall 303, the sensing surface area dependsupon the distance of this extension and the circumference of thereaction region 301, and can be relatively large. As a result, low noisechemical sensors 350, 351 can be provided in a high density array, suchthat the characteristics of reactions can be accurately detected.

During manufacturing and/or operation of the device, a thin oxide of thematerial of the electrically conductive sidewall spacer 370 may be grownon the inner surface 371 which acts as a sensing material (e.g. anion-sensitive sensing material) for the chemical sensor 350. Similarly,a thin oxide of the material of the electrically conductive sensor plate320 may be grown on the upper surface 331 which also acts as a sensingmaterial. Whether an oxide is formed depends on the conductivematerials, the manufacturing processes performed, and the conditionsunder which the device is operated.

In some embodiments, the sidewall spacer 370 and the upper layer of thesensor plate 320 may be the same material. For example, in oneembodiment the sidewall spacer 370 and the upper layer of the sensorplate 320 may each be titanium nitride, and titanium oxide or titaniumoxynitride may be grown on the inner surface 371 and the upper surface331 during manufacturing and/or during exposure to solutions during use.

Alternatively, the sidewall spacer 370 and the upper layer of the sensorplate 320 may comprise different materials. In such a case, the upperlayer of the sensor plate 320 may be a material that provides relativelyhigh buffering of the particular ions of interest (e.g. hydrogen ions)compared to material of the sidewall spacer 370 for the given operatingconditions. For example, in one embodiment in which the operational pHlevel of the solution is between 7 and 9, the upper layer of the sensorplate 320 is titanium nitride, while the sidewall spacer 320 is hafnium.As described in more detail below, the use of different materials forthe sidewall spacer 370 and the upper layer of the sensor plate 320 canenable the SNR of the sensor output signal of the chemical sensor 350 tobe maximized.

In the illustrated example, the sidewall spacer 370 and the sensor plate320 are each shown as single layers of material. More generally, thesidewall spacer 370 and the sensor plate 320 may each comprise one ormore layers of a variety of electrically conductive materials, such asmetals or ceramics, depending upon the implementation. The conductivematerial can be for example a metallic material or alloy thereof, or canbe a ceramic material, or a combination thereof. An exemplary metallicmaterial includes one of aluminum, copper, nickel, titanium, silver,gold, platinum, hafnium, lanthanum, tantalum, tungsten, iridium,zirconium, palladium, or a combination thereof. An exemplary ceramicmaterial includes one of titanium nitride, titanium aluminum nitride,titanium oxynitride, tantalum nitride, or a combination thereof.

In some alternative embodiments, an additional conformal sensingmaterial (not shown) is deposited on the inner surface 371 of theconductive sidewall spacer 370 and on the upper surface 331 of thesensor plate 320. The sensing material may comprise one or more of avariety of different materials to facilitate sensitivity to particularions. For example, silicon nitride or silicon oxynitride, as well asmetal oxides such as silicon oxide, aluminum or tantalum oxides,generally provide sensitivity to hydrogen ions, whereas sensingmaterials comprising polyvinyl chloride containing valinomycin providesensitivity to potassium ions. Materials sensitive to other ions such assodium, silver, iron, bromine, iodine, calcium, and nitrate may also beused, depending upon the implementation.

As shown in the plan view of FIG. 3B, the inner surface 371 of thesidewall spacer 370 surrounds the reaction region 301. In theillustrated example the opening and the reaction region 301 havecircular cross sections. Alternatively, these may be non-circular. Forexample, the cross-section may be square, rectangular, hexagonal, orirregularly shaped.

Referring back to FIG. 3A, in operation, reactants, wash solutions, andother reagents may move in and out of the reaction region 301 by adiffusion mechanism 340. The chemical sensor 350 is responsive to (andgenerates an output signal related to) the amount of a charge 324proximate to the sidewall spacer 370 and the sensor plate 320. Thepresence of charge 324 in an analyte solution alters the surfacepotential at the interface between the analyte solution and the sidewallspacer 370/sensor plate 320, due to the protonation or deprotonation ofsurface charge groups caused by the ions present in the analytesolution. Changes in the charge 324 cause changes in the voltage on thefloating gate structure 318, which in turn changes in the thresholdvoltage of the transistor of the chemical sensor 350. This change inthreshold voltage can be measured by measuring the current in thechannel region 323 between the source region 321 and a drain region 322.As a result, the chemical sensor 350 can be used directly to provide acurrent-based output signal on an array line connected to the sourceregion 321 or drain region 322, or indirectly with additional circuitryto provide a voltage-based output signal.

The amplitude of the desired signal detected in response to the charge324 is a superposition of the interface between the analyte solution andthe sidewall spacer 370, and the interface between the analyte solutionand the sensor plate 320. Because the charge is more highly concentratednear the bottom of the reaction region 301, in some embodiments thematerial for the sensor plate 320 is chosen which has a relatively highbuffering capacity for the particular ions of interest (e.g. hydrogenions) for the given operating conditions. In doing so, the sensor plate320 can maximally detect signal from an area of high chargeconcentration.

The buffering capacity of the material of the sidewall spacer 370 is atradeoff between the amplitude of the desired signal detected inresponse to the charge 324, and the fluidic noise due to randomfluctuation of charge at the interface between the analyte solution andthe sidewall spacer 370/sensor plate 320. A relatively high bufferingmaterial for the sidewall spacer 370 increases the effective fluidicinterface area for the chemical sensor 350, which reduces the fluidicnoise. However, since the surface density of the charge 324 decreaseswith distance from the bottom of the reaction region, the high bufferingmaterial detects a greater proportion of the signal from areas havinglower charge concentration, which can reduce the overall amplitude ofthe desired signal detected by the sensor 350. In contrast, a relativelylow buffering material for the sidewall spacer 370 reduces the effectivesensing surface area and thus increases the fluidic noise, but alsoincreases the overall amplitude of the desired signal detected by thesensor 350 due to a greater proportion of the signal being contributedby the sensor plate 320.

For a very small sensing surface area, Applicants have found that thefluidic noise changes as a function of the sensing surface areadifferently than the amplitude of the desired signal. Because the SNR ofthe sensor output signal is the ratio of these two quantities, there isan optimal material for the sidewall spacer 370 having bufferingcharacteristics at which SNR is maximum.

The material having the optimal buffering capacity for the sidewallspacer 370 can vary from embodiment to embodiment depending on thematerial characteristics of the sensor plate 320, the volume, shape,aspect ratio (such as base width-to-well depth ratio), and otherdimensional characteristics of the reaction regions, the nature of thereaction taking place, as well as the reagents, byproducts, or labelingtechniques (if any) that are employed. The optimal material may forexample be determined empirically.

In an embodiment, reactions carried out in the reaction region 301 canbe analytical reactions to identify or determine characteristics orproperties of an analyte of interest. Such reactions can generatedirectly or indirectly byproducts that affect the amount of chargeadjacent to the sensor plate 320 and the sidewall spacer 370. If suchbyproducts are produced in small amounts or rapidly decay or react withother constituents, multiple copies of the same analyte may be analyzedin the reaction region 301 at the same time in order to increase theoutput signal generated. In an embodiment, multiple copies of an analytemay be attached to a solid phase support 312, either before or afterdeposition into the reaction region 301. The solid phase support 312 maybe microparticles, nanoparticles, beads, solid or porous comprisinggels, or the like. For simplicity and ease of explanation, solid phasesupport 312 is also referred herein as a particle. For a nucleic acidanalyte, multiple, connected copies may be made by rolling circleamplification (RCA), exponential RCA, or like techniques, to produce anamplicon without the need of a solid support.

In various exemplary embodiments, the methods, systems, and computerreadable media described herein may advantageously be used to processand/or analyze data and signals obtained from electronic orcharged-based nucleic acid sequencing. In electronic or charged-basedsequencing (such as, pH-based sequencing), a nucleotide incorporationevent may be determined by detecting ions (e.g., hydrogen ions) that aregenerated as natural by-products of polymerase-catalyzed nucleotideextension reactions. This may be used to sequence a sample or templatenucleic acid, which may be a fragment of a nucleic acid sequence ofinterest, for example, and which may be directly or indirectly attachedas a clonal population to a solid support, such as a particle,microparticle, bead, etc. The sample or template nucleic acid may beoperably associated to a primer and polymerase and may be subjected torepeated cycles or “flows” of deoxynucleoside triphosphate (“dNTP”)addition (which may be referred to herein as “nucleotide flows” fromwhich nucleotide incorporations may result) and washing. The primer maybe annealed to the sample or template so that the primer's 3′ end can beextended by a polymerase whenever dNTPs complementary to the next basein the template are added. Then, based on the known sequence ofnucleotide flows and on measured output signals of the chemical sensorsindicative of ion concentration during each nucleotide flow, theidentity of the type, sequence and number of nucleotide(s) associatedwith a sample nucleic acid present in a reaction region coupled to achemical sensor can be determined.

FIGS. 4 to 7 illustrate stages in a manufacturing process for forming anarray of chemical sensors and corresponding well structures according toan exemplary embodiment.

FIG. 4 illustrates a first stage of forming a structure including adielectric material 310 on the sensor plate 320 of the field effecttransistor of the chemical sensor 350. The structure in FIG. 4 can beformed by depositing a layer of gate dielectric material on thesemiconductor substrate 354, and depositing a layer of polysilicon (orother electrically conductive material) on the layer of gate dielectricmaterial. The layer of polysilicon and the layer gate dielectricmaterial can then be etched using an etch mask to form the gatedielectric elements (e.g. gate dielectric 352) and the lowermostconductive material element of the floating gate structures. Followingformation of an ion-implantation mask, ion implantation can then beperformed to form the source and drain regions (e.g. source region 321and a drain region 322) of the chemical sensors.

A first layer of the dielectric material 319 can then be deposited overthe lowermost conductive material elements. Conductive plugs can then beformed within vias etched in the first layer of dielectric material 319to contact the lowermost conductive material elements of the floatinggate structures. A layer of conductive material can then be deposited onthe first layer of the dielectric material 319 and patterned to formsecond conductive material elements electrically connected to theconductive plugs. This process can then be repeated multiple times toform the completed floating gate structure 318 shown in FIG. 4.Alternatively, other and/or additional techniques may be performed toform the structure.

Forming the structure in FIG. 4 can also include forming additionalelements such as array lines (e.g. word lines, bit lines, etc.) foraccessing the chemical sensors, additional doped regions in thesubstrate 354, and other circuitry (e.g. access circuitry, biascircuitry etc.) used to operate the chemical sensors, depending upon thedevice and array configuration in which the chemical sensors describedherein are implemented. In some embodiments, the elements of thestructure may for example be manufactured using techniques described inU.S. Patent Application Publication No. 2010/0300559, No. 2010/0197507,No. 2010/0301398, No. 2010/0300895, No. 2010/0137143, and No.2009/0026082, and U.S. Pat. No. 7,575,865, each which are incorporatedby reference herein.

Next, the dielectric material 310 of the structure in FIG. 4 is etchedto form openings 500, 502 extending to the upper surfaces of thefloating gate structures of the chemical sensors 350, 351, resulting inthe structure illustrated in FIG. 5.

The openings 500, 502 may for example be formed by using a lithographicprocess to pattern a layer of photoresist on the dielectric material 310to define the locations of the openings 500, 502, and thenanisotropically etching the dielectric material 310 using the patternedphotoreist as an etch mask. The anisotropic etching of the dielectricmaterial 310 may for example be a dry etch process, such as a fluorinebased Reactive Ion Etching (RIE) process.

In the illustrated embodiment, the openings 500, 502 are separated by adistance that 530 that is equal to their width 520. Alternatively, theseparation distance 530 between adjacent openings may be less than thewidth 520. For example, the separation distance 530 may be a minimumfeature size for the process (e.g. a lithographic process) used to formthe openings 500, 502. In such a case, the distance 530 may besignificantly less than the width 520.

Next, a conformal layer of conductive material 600 is deposited on thestructure illustrated in FIG. 5, resulting in the structure illustratedin FIG. 6. The conductive material 600 comprises one or more layers ofelectrically conductive material. For example, the conductive material500 may be a layer of titanium nitride, or a layer of titanium.Alternatively, other and/or additional conductive materials may be used,such as those described above with reference to the sidewall spacer 370.In addition, more than one layer of conductive material may bedeposited.

The conductive material 600 may be deposited using various techniques,such as sputtering, reactive sputtering, atomic layer deposition (ALD),low pressure chemical vapor deposition (LPCVD), plasma enhanced chemicalvapor deposition (PECVD), metal organic chemical vapor deposition(MOCVD) etc.

Next, an anisotropic etching process is performed on the conductivematerial 600 illustrated in FIG. 6 to form sidewall spacers 370, 700within the openings 500, 502, resulting in the structure illustrated inFIG. 7. The anisotropic etching process removes the material of thelayer of conductive material 600 on horizontal surfaces at a faster ratethan material on vertical surfaces. In doing so, the anisotropic etchingprocess exposes the upper surface 331 of the sensor plate 320, as wellas the upper surface of the dielectric material 310. The anisotropicetching process may for example be performed using a RIE or other plasmaetching process. Alternatively, other etching processes may be used.

While the present invention is disclosed by reference to the preferredembodiments and examples detailed above, it is to be understood thatthese examples are intended in an illustrative rather than in a limitingsense. It is contemplated that modifications and combinations willreadily occur to those skilled in the art, which modifications andcombinations will be within the spirit of the invention and the scope ofthe following claims.

What is claimed is:
 1. A chemical sensor comprising: achemically-sensitive field effect transistor including a floating gateconductor having an upper surface; a dielectric material defining anopening extending to the upper surface of the floating gate conductor;and a conductive sidewall spacer on a sidewall of the opening andcontacting the upper surface of the floating gate conductor; wherein thechemically-sensitive field effect transistor includes a floating gatestructure comprising a plurality of conductors electrically coupled toone another and separated by dielectric layers, and the floating gateconductor is an uppermost conductor in the plurality of conductors. 2.The chemical sensor of claim 1, wherein the conductive sidewall spacerincludes an inner surface surrounding a reaction region for the chemicalsensor.
 3. The chemical sensor of claim 1, wherein the conductivesidewall spacer comprises an electrically conductive material, and aninner surface of the conductive sidewall spacer includes an oxide of theelectrically conductive material.
 4. The chemical sensor of claim 1,wherein a sensing surface for the chemical sensor includes an innersurface of the conductive sidewall spacer and the upper surface of thefloating gate conductor.
 5. The chemical sensor of claim 1, wherein theconductive sidewall spacer comprises material different from material atthe upper surface of the floating gate conductor.
 6. The chemical sensorof claim 1, wherein the chemically-sensitive field effect transistorgenerates a sensor signal in response to a chemical reaction occurringproximate to the conductive sidewall spacer.
 7. The chemical sensor ofclaim 1, further comprising a microfluidic structure in fluid flowcommunication with the chemically-sensitive field effect transistor, andarranged to deliver analytes for sequencing.
 8. The chemical sensor ofclaim 2, wherein the inner surface of the conductive sidewall spacer isan outer surface of the reaction region, and the upper surface of thefloating gate conductor is a bottom surface of the reaction region. 9.The chemical sensor of claim 4, wherein the sensing surface is sensitiveto hydrogen ions.
 10. The chemical sensor of claim 6, wherein thechemical reaction is a sequencing reaction.